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Foundational Competencies and Responsibilities of a Research Software Engineer

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arXiv 2023年

作者： Goth, Florian Alves, Renato Braun, Matthias Castro, Leyla Jael Chourdakis, Gerasimos Christ, Simon Cohen, Jeremy Druskat, Stephan Erxleben, Fredo Grad, Jean-Noël Hagdorn, Magnus Hodges, Toby Juckeland, Guido Kempf, Dominic Lamprecht, Anna-Lena Linxweiler, Jan Löffler, Frank Martone, Michele Schwarzmeier, Moritz Seibold, Heidi Thiele, Jan Philipp Waldow, Harald von Wittke, Samantha Institute for Theoretical Physics and Astrophysics University of Würzburg Germany European Molecular Biology Laboratory Heidelberg Germany Cluster of Excellence IntCDC University of Stuttgart Germany ZB MED Information Centre for Life Sciences Cologne Germany School of Computation Information and Technology Technical University of Munich Garching Germany Institute for Parallel and Distributed Systems University of Stuttgart Stuttgart Germany Leibniz University Hannover Department of Cell Biology and Biophysics Computational Biology Germany Imperial College London London United Kingdom Institute for Software Technology Berlin Germany Humboldt-Universität zu Berlin Department of Computer Science Berlin Germany Helmholtz-Zentrum Dresden-Rossendorf Germany Institute for Computational Physics University of Stuttgart Germany Geschäftsbereich IT Charité Universitätsmedizin Berlin Germany The Carpentries United States Heidelberg University Scientific Software Center Germany Institute of Computer Science University of Potsdam Germany Technische Universität Braunschweig Germany Michael Stifel Center Jena Friedrich Schiller University Jena Germany Leibniz Supercomputing Centre Garching Germany Mathematical Modeling and Analysis TU Darmstadt Germany IGDORE Munich Germany Weierstrass Institute Berlin Germany Leibniz University Hannover Institute of Applied Mathematics Scientific Computing Hannover Germany Johann Heinrich von Thünen Institute Centre for Information Management Germany

The term Research Software Engineer, or RSE, emerged a little over 10 years ago as a way to represent individuals working in the research community but focusing on software development. The term has been widely adopted and there are a number of high-level definitions of what an RSE is. However, the roles of RSEs vary depending on the institutional context they work in. At one end of the spectrum, RSE roles may look similar to a traditional research role. At the other extreme, they resemble that of a software engineer in industry. Most RSE roles inhabit the space between these two extremes. Therefore, providing a straightforward, comprehensive definition of what an RSE does and what experience, skills and competencies are required to become one is challenging. In this community paper we define the broad notion of what an RSE is, explore the different types of work they undertake, and define a list of foundational competencies as well as values that outline the general profile of an RSE. Further research and training can build upon this foundation of skills and focus on various aspects in greater detail. We expect that graduates and practitioners will have a larger and more diverse set of skills than outlined here. On this basis, we elaborate on the progression of these skills along different dimensions. We look at specific types of RSE roles, propose recommendations for organisations, and give examples of future specialisations. An appendix details how existing curricula fit into this framework. © 2023, CC BY.

关键词： Computer aided software engineering

Adaptive finite element approximation for steady-state poisson-nernst-planck equations

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arXiv 2020年

作者： Hao, Tingting Ma, Manman Xu, Xuejun School of Mathematical Sciences Tongji University Shanghai200092 China School of Mathematical Sciences Tongji University Shanghai200092 China LSEC Institute of Computational Mathematics and Scientific/Engineering Computing Academy of Mathematics and System Sciences Chinese Academy of Sciences Beijing100190 China

In this paper, we develop an adaptive finite element method for the nonlinear steady-state Poisson-Nernst-Planck equations, where the spatial adaptivity for geometrical singularities and boundary layer effects are mainly considered. As a key contribution, the steady-state Poisson-Nernst-Planck equations are studied systematically and rigorous analysis for a residual-based a posteriori error estimate of the nonlinear system is presented. With the help of Schauder fixed point theorem, we show the solution existence and uniqueness of the linearized system derived by taking G−derivatives of the nonlinear system, followed by the proof of the relationship between the error of solution and the a posteriori error estimator η. Numerical experiments are given to validate the efficiency of the a posteriori error estimator and demonstrate the expected rate of convergence. In the further tests, adaptive mesh refinements for geometrical singularities and boundary layer effects are successfully observed. Copyright © 2020, The Authors. All rights reserved.

关键词： Nonlinear systems

Novel design and analysis of generalized FE methods based on locally optimal spectral approximations

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arXiv 2021年

作者： Ma, Chupeng Scheichl, Robert Dodwell, Tim J. Institute for Applied Mathematics Interdisciplinary Center for Scientific Computing Heidelberg University Im Neuenheimer Feld 205 Heidelberg69120 Germany College of Engineering Mathematics and Physical Sciences University of Exeter ExeterEX4 4PY United Kingdom The Alan Turing Institute LondonNW1 2DB United Kingdom

In this paper, the generalized finite element method (GFEM) for solving second order elliptic equations with rough coefficients is studied. New optimal local approximation spaces for GFEMs based on local eigenvalue problems involving a partition of unity are presented. These new spaces have advantages over those proposed in [I. Babuska and R. Lipton, Multiscale Model. Simul., 9 (2011), pp. 373–406]. First, in addition to a nearly exponential decay rate of the local approximation errors with respect to the dimensions of the local spaces, the rate of convergence with respect to the size of the oversampling region is also established. Second, the theoretical results hold for problems with mixed boundary conditions defined on general Lipschitz domains. Finally, an efficient and easy-to-implement technique for generating the discrete A-harmonic spaces is proposed which relies on solving an eigenvalue problem associated with the Dirichlet-to-Neumann operator, leading to a substantial reduction in computational cost. Numerical experiments are presented to support the theoretical analysis and to confirm the effectiveness of the new method. Copyright © 2021, The Authors. All rights reserved.

关键词： Eigenvalues and eigenfunctions

The elastic inclusion problem in the (amplitude) phase field crystal model

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arXiv 2021年

作者： Salvalaglio, Marco Chockalingam, Karthikeyan Voigt, Axel Dörfler, Willy Institute of Scientific Computing TU Dresden Dresden01062 Germany Dresden Center for Computational Materials Science TU Dresden Dresden01062 Germany Science and Technology Facilities Council Daresbury Laboratory Daresbury Science and Innovation Campus Warrington Cheshire WA4 4AD United Kingdom Institute for Applied and Numerical Mathematics Karlsruhe Institute of Technology Karlsruhe76131 Germany

In many processes for crystalline materials such as precipitation, heteroepitaxy, alloying, and phase transformation, lattice expansion or compression of embedded domains occurs. This can significantly alter the mechanical response of the material. Typically, these phenomena are studied macroscopically, thus neglecting the underlying microscopic structure. Here we present the prototypical case of an elastic inclusion described by a mesoscale model, namely a coarse-grained phase-field crystal model. A spatially-dependent parameter is introduced into the free energy functional to control the local spacing of the lattice structure, effectively prescribing an eigenstrain. The stress field obtained for an elastic inclusion in a 2D triangular lattice is shown to match well with the analytic solution of the Eshelby inclusion problem. Copyright © 2021, The Authors. All rights reserved.

关键词： Free energy

Overview of couplet scoring in content-focused physics assessments

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arXiv 2023年

作者： Vignal, Michael Geschwind, Gayle Caballero, Marcos D. Lewandowski, H.J. JILA National Institute of Standards and Technology the University of Colorado BoulderCO80309 United States Department of Physics University of Colorado 390 UCB BoulderCO80309 United States Department of Physics Willamette University 900 State Street SalemOR97301 United States Department of Physics & Astronomy CREATE for STEM Institute Michigan State University East LansingMI48824 United States Department of Computational Mathematics Science & Engineering Michigan State University East LansingMI48824 United States Department of Physics Center for Computing in Science Education University of Oslo Oslo0315 Norway

Content-focused research-based assessment instruments typically use items (i.e., questions) as the unit of assessment for scoring, reporting, and validation. Couplet scoring employs an alternative unit of assessment called a couplet, which is essentially an item viewed and scored through the lens of a specific assessment objective. With couplet scoring, a single item may have more than one assessment objective and therefore more than one couplet and thus more than one score. We outline the components of traditional item scoring, discuss couplet scoring and its benefits, and use both a recently developed content research-based assessment instrument and an existing one to ground our discussion. © 2023, CC BY.

关键词： Uncertainty analysis

On the implementation of a robust and efficient finite element-based parallel solver for the compressible Navier-Stokes equations

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arXiv 2021年

作者： Guermond, Jean-Luc Kronbichler, Martin Maier, Matthias Popov, Bojan Tomas, Ignacio Department of Mathematics Texas A&M University 3368 College StationTX77843 United States Institute for Computational Mechanics Department for Mechanical Engineering Technical University of Munich Germany Division of Scientific Computing Department of Information Technology Uppsala University Sweden Sandia National Laboratories P.O. Box 5800 MS 1320 AlbuquerqueNM87185-1320 United States

This paper describes in detail the implementation of a finite element technique for solving the compressible Navier-Stokes equations that is provably robust and demonstrates excellent performance on modern computer hardware. The method is second-order accurate in time and space. Robustness here means that the method is proved to be invariant domain preserving under the hyperbolic CFL time step restriction, and the method delivers results that are reproducible. The proposed technique is shown to be accurate on challenging 2D and 3D realistic *** Codes 35L65, 65M60, 65M12, 65N30 Copyright © 2021, The Authors. All rights reserved.

关键词： Finite element method

ParaDiag: Parallel-in-time algorithms based on the diagonalization technique

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arXiv 2020年

作者： Gander, Martin J. Liu, Jun Wu, Shu-Lin Yue, Xiaoqiang Zhou, Tao Section of Mathematics University of Geneva GenevaCH-1211 Switzerland Department of Mathematics and Statistics Southern Illinois University Edwardsville EdwardsvilleIL62026 United States School of Mathematics and Statistics Northeast Normal University Changchun130024 China School of Mathematics and Computational Science Xiangtan University Xiangtan411105 China Institute of Computational Mathematics and Scientific/Engineering Computing AMSS Chinese Academy of Sciences Beijing China

In 2008, Maday and Rønquist introduced an interesting new approach for the direct parallel-in-time (PinT) solution of time-dependent PDEs. The idea is to diagonalize the time stepping matrix, keeping the matrices for the space discretization unchanged, and then to solve all time steps in parallel. Since then, several variants appeared, and we call these closely related algorithms ParaDiag algorithms. ParaDiag algorithms in the literature can be classified into two groups: We will explain the basic features of each group in this note. To have concrete examples, we will introduce ParaDiag-I and ParaDiag-II for the advection-diffusion equation. We will also introduce ParaDiag-II for the wave equation and an optimal control problem for the wave equation. We could have used the advection-diffusion equation as well to illustrate ParaDiag-II, but wave equations are known to cause problems for certain PinT algorithms and thus constitute an especially interesting example for which ParaDiag algorithms were tested. We show the main known theoretical results in each case, and also provide Matlab codes for testing. The goal of the Matlab codes is to help the interested reader understand the key features of the ParaDiag algorithms, without intention to be highly tuned for efficiency and/or low memory use. We also provide speedup measurements of ParaDiag algorithms for a 2D linear advection-diffusion equation. These results are obtained on the Tianhe-1 supercomputer in China and the SIUE Campus Cluster in the US, which is a multi-array, configurable and cooperative parallel system, and we compare these results to the performance of parareal and MGRiT, two widely used PinT algorithms. In a forthcoming update of this note, we will provide more material on ParaDiag algorithms, in particular further Matlab codes and parallel computing results, also for more realistic applications. Copyright © 2020, The Authors. All rights reserved.

关键词： Advection

Doubly degenerate diffuse interface models of anisotropic surface diffusion

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arXiv 2020年

作者： Salvalaglio, Marco Selch, Maximilian Voigt, Axel Wise, Steven M. Institute of Scientific Computing Department of Mathematics Tu Dresden Dresden01062 Germany Dresden Center for Computational Materials Science Tu Dresden Dresden01062 Germany Department of Mathematics University of Tennessee KnoxvilleTN37996 United States

We extend the doubly degenerate Cahn-Hilliard (DDCH) models for isotropic surface diffusion1, which yield more accurate approximations than classical degenerate Cahn-Hilliard (DCH) models, to the anisotropic case. We consider both weak and strong anisotropies and demonstrate the capabilities of the approach for these cases numerically. The proposed model provides a variational and energy dissipative approach for anisotropic surface diffusion, enabling large scale simulations with material-specific parameters. Copyright © 2020, The Authors. All rights reserved.

关键词： Anisotropy

***: A Comprehensive Genomic Visualisation Database for Malaysian Species

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***: A Comprehensive Genomic Visualisation Database for Mala...

computing (ICOCO), IEEE International Conference on

作者： Vei Siang Chan Farhan Bin Mohamed Faezah Mohd Salleh Andres Iglesias Alina Binti Wagiran Ali Bin Selamat School of Computing Faculty of Engineering Universiti Teknologi Malaysia Johor Bahru Malaysia Media and Game Innovation Center of Excellence Universiti Teknologi Malaysia Johor Bahru Malaysia Dept. of Biosciences Faculty of Science Universiti Teknologi Malaysia Johor Bahru Malaysia Dept. of Applied Mathematics and Computational Sciences University of Cantabria Santander Spain Malaysia-Japan International Institute of Technology University of Technology Malaysia Kuala Lumpur Malaysia

ISBN: (纸本)9781665489973

Malaysia is one of the most megadiverse regions in the world. Therefore, it is important to record these rich biodiversity data to safeguard and improve national conservation efforts. However, the lack of nationwide genomic sequencing hampers a more sophisticated species identification, data management, and analytics activities. Thus, this project aims to design and implement ***, a comprehensive one-stop online DNA reference database with integrated DNA visualisation and digital references to allow the users to search, retrieve and analyse the collected DNA sequencing data interactively. This paper documented the system architecture and implementation methods to create ***. The results of *** can display taxonomy information of biodiversity in the web’s user interfaces and visualise the complex set of DNA data to allow new insights. Lastly, the authors identified several future works to improve *** including improve user interaction, add visualisation methods to support more bioinformatics tasks, and conduct formal user evaluation.

关键词： Sequential analysis Annotations Taxonomy Data visualization DNA Genomics Systems architecture